PHYLOGENY MAGNITUDE OF Mycobacterium tuberculosis BASED ON GENOMIC ANALYSIS

Budi Yanti; Mulyadi Mulyadi; Soetjipto Soetjipto; Ni Made Mertaniasih; Muhammad Amin

doi:10.20885/JKKI.Vol11.Iss2.art12

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October 15, 2019

Accepted

August 31, 2020

Published

August 31, 2020

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Abstract

Mycobacterium tuberculosis (MTB) is mostly found in humans, and it can cause more than two million deaths each year with increasing morbidity. Although lineages of MTB show identical nucleotide relationships, they have different characteristics such as evolution, transmission, drug resistance, host interaction, latency, and vaccine effectiveness. It is necessary to have better understanding of MTB relationships based on similarities in genome sizes and phylogenetic analysis. This paper observes the relationships of MTB based on nucleotide through phylogenetic frameworks. The MTB species consist of six lineages, and each lineage has various size of genomes . This difference contributes to virulence of MTB affecting levels of severity, morbidity, and mortality of diseases. Genetic diversity of MTB can contribute to global threats in the world such as outbreak of tuberculosis, Multi Drug Resistant (MDR) and Extensively Drug Resistant (XDR) tuberculosis.

Keywords

Mycobacterium tuberculosis multi drug resistant phylogenetic

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Author Biography

Budi Yanti, Department of Pulmonology and Respiratory Medicine, School of Medicine, Universitas Syiah Kuala, Banda Aceh

Pulmonolgy and Respiratory Medicine

How to Cite

Yanti, B., Mulyadi, M., Soetjipto, S., Mertaniasih, N. M., & Amin, M. (2020). Phylogeny magnitude of Mycobacterium tuberculosis based on genomic analysis. JKKI : Jurnal Kedokteran Dan Kesehatan Indonesia, 11(2), 191–197. https://doi.org/10.20885/JKKI.Vol11.Iss2.art12

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References

World Health Organization. Global tuberculosis report 2019. Geneva; 2019.
Pusat data dan Informasi-Kementrian Kesehatan Republik Indonesia. Infodatin Tuberkulosis 2018. 2018. www.pusdatin.kemkes.go.id
Merker M, Kohl T, Niemann S, Supply P. The evolution of strain typing in the Mycobacterium tuberculosis complex. In: Gagneux S, editor. Strain variation in the Mycobacterium tuberculosis complex: Its role in biology, epidemiology and control. Geneva: Springer; 2017. p. 43–78.
Lönnroth K, Jaramillo E, Williams BG, Dye C, Raviglione M. Drivers of tuberculosis epidemics: The role of risk factors and social determinants. Social Science & Medicine. 2009; 68(12):2240–6.
Abel L, El-Baghdadi J, Bousfiha AA, Casanova J-L, Schurr E. Human genetics of tuberculosis: A long and winding road. Philosophical Transactions of the Royal Society B: Biological Sciences. 2014;369(1645):20130428. https://doi.org/10.1098/rstb.2013.0428
Dunn CW, Luo X, Wu Z. Phylogenetic analysis of gene expression. Integrative and Comparative Biology. 2013;53(5):847–56.
Khan NH, Ahsan M, Yoshizawa S, Hosoya S, Yokota A, Kogure K. Multilocus Sequence Typing and Phylogenetic Analyses of Pseudomonas aeruginosa Isolates from the Ocean. Applied and Environmental Microbiology. 2008;74(20):6194 LP – 6205.
Shitikov E, Kolchenko S, Mokrousov I, Bespyatykh J, Ischenko D, Ilina E, et al. Evolutionary pathway analysis and unified classification of East Asian lineage of Mycobacterium tuberculosis. Scientific Reports. 2017;7(1):9227.
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537–44.
Roychowdhury T, Mandal S, Bhattacharya A. Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Scientific Reports. 2015;5:12567.
Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evolutionary Biology. 2006;6:95.
Coscolla M, Gagneux S. Does M. tuberculosis genomic diversity explain disease diversity?. Drug Discovery Today: Disease Mechanisms. 2010;7(1):e43–59.
Gasperskaja E, Kucinskas V. The most common technologies and tools for functional genome analysis. Acta medica Lituaniva. 2017;24(1):1–11.
Comas I, Homolka S, Niemann S, Gagneux S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One. 2009;4(11):e7815.
Richter C, Chang JT, Fineran PC. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems. Viruses. 2012;4(10):2291–311.
Parkinson N, Bryant R, Bew J, Conyers C, Stones R, Alcock M, et al. Application of variable-number tandem-repeat typing to discriminate Ralstonia solanacearum strains associated with English watercourses and disease outbreaks. Applied and Environmental Microbiology. 2013;79(19):6016 LP – 6022.
Jagielski T, Van Ingen J, Rastogi N, Dziadek J, Mazur PK, Bielecki J. Current methods in the molecular typing of mycobacterium tuberculosis and other Mycobacteria. BioMed Research International. 2014;2014:1–12.
Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong BC, Narayanan S, et al. Variable host–pathogen compatibility in Mycobacterium tuberculosis. proceeding of the national academy of sciences of the united states of America. 2006;103(8):2869 LP – 2873.
Bañuls AL, Sanou A, Van Anh NT, Godreuil S. Mycobacterium tuberculosis: Ecology and evolution of a human bacterium. Journal of Medical Microbiology. 2015;64(11):1261–9.
Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global?dissemination. proceeding of the national academy of sciences of the united states of America. 1997;94(18):9869 LP – 9874.
Lu B, Dong Hy, Zhao Xq, Liu Zg, Liu Hc, Zhang Yy, et al. A new multilocus sequence analysis scheme for Mycobacterium tuberculosis. Biomedical and Environmental Sciences. 2012;25(6):620–9.
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLOS Biology. 2008;6(12):e311.
Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, et al. Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. Journal of Clinical Microbiology. 2007;45(1):39–46.
Gutacker MM, Mathema B, Soini H, Shashkina E, Kreiswirth BN, Graviss EA, et al. Single-nucleotide polymorphism–based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. Journal of the Infectious Diseases. 2006;193(1):121–8.
Keats BJB, Sherman SL. Chapter 13 - Population genetics. In: Rimoin D, Pyeritz R, Korf BBT-E and RP and P of MG, editors. Oxford: Academic Press; 2013. p. 1–12. www.sciencedirect.com/science/article/pii/B978012383834600015X
Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, et al. Out-of-Africa migration and neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics 2013;45(10):1176–82.
Reiling N, Homolka S, Walter K, Brandenburg J, Niwinski L, Ernst M, et al. Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice. MBio. 2013;4(4):e00250-13.
Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, et al. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. Journal of Clinical Microbiology. 2003;41(5):1963–70.
Bhargavi M. Multidrug Resistance in Tuberculosis: An overview. International Journal of Pharmaceutical. 2014;4(3):157–63.
Regmi SM, Coker OO, Kulawonganunchai S, Tongsima S, Prammananan T, Viratyosin W, et al. Polymorphisms in drug-resistant-related genes shared among drug-resistant and pan-susceptible strains of sequence type 10, Beijing family of Mycobacterium tuberculosis. International Journal of Mycobacteriology. 2015;4(1):67–72.
Brown T, Nikolayevskyy V, Velji P, Drobniewski F. Associations between Mycobacterium tuberculosis strains and phenotypes. Emerging Infectious Diseases. 2010;16(2):272–80.

References

World Health Organization. Global tuberculosis report 2019. Geneva; 2019.

Pusat data dan Informasi-Kementrian Kesehatan Republik Indonesia. Infodatin Tuberkulosis 2018. 2018. www.pusdatin.kemkes.go.id

Merker M, Kohl T, Niemann S, Supply P. The evolution of strain typing in the Mycobacterium tuberculosis complex. In: Gagneux S, editor. Strain variation in the Mycobacterium tuberculosis complex: Its role in biology, epidemiology and control. Geneva: Springer; 2017. p. 43–78.

Lönnroth K, Jaramillo E, Williams BG, Dye C, Raviglione M. Drivers of tuberculosis epidemics: The role of risk factors and social determinants. Social Science & Medicine. 2009; 68(12):2240–6.

Abel L, El-Baghdadi J, Bousfiha AA, Casanova J-L, Schurr E. Human genetics of tuberculosis: A long and winding road. Philosophical Transactions of the Royal Society B: Biological Sciences. 2014;369(1645):20130428. https://doi.org/10.1098/rstb.2013.0428

Dunn CW, Luo X, Wu Z. Phylogenetic analysis of gene expression. Integrative and Comparative Biology. 2013;53(5):847–56.

Khan NH, Ahsan M, Yoshizawa S, Hosoya S, Yokota A, Kogure K. Multilocus Sequence Typing and Phylogenetic Analyses of Pseudomonas aeruginosa Isolates from the Ocean. Applied and Environmental Microbiology. 2008;74(20):6194 LP – 6205.

Shitikov E, Kolchenko S, Mokrousov I, Bespyatykh J, Ischenko D, Ilina E, et al. Evolutionary pathway analysis and unified classification of East Asian lineage of Mycobacterium tuberculosis. Scientific Reports. 2017;7(1):9227.

Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537–44.

Roychowdhury T, Mandal S, Bhattacharya A. Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Scientific Reports. 2015;5:12567.

Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evolutionary Biology. 2006;6:95.

Coscolla M, Gagneux S. Does M. tuberculosis genomic diversity explain disease diversity?. Drug Discovery Today: Disease Mechanisms. 2010;7(1):e43–59.

Gasperskaja E, Kucinskas V. The most common technologies and tools for functional genome analysis. Acta medica Lituaniva. 2017;24(1):1–11.

Comas I, Homolka S, Niemann S, Gagneux S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One. 2009;4(11):e7815.

Richter C, Chang JT, Fineran PC. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems. Viruses. 2012;4(10):2291–311.

Parkinson N, Bryant R, Bew J, Conyers C, Stones R, Alcock M, et al. Application of variable-number tandem-repeat typing to discriminate Ralstonia solanacearum strains associated with English watercourses and disease outbreaks. Applied and Environmental Microbiology. 2013;79(19):6016 LP – 6022.

Jagielski T, Van Ingen J, Rastogi N, Dziadek J, Mazur PK, Bielecki J. Current methods in the molecular typing of mycobacterium tuberculosis and other Mycobacteria. BioMed Research International. 2014;2014:1–12.

Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong BC, Narayanan S, et al. Variable host–pathogen compatibility in Mycobacterium tuberculosis. proceeding of the national academy of sciences of the united states of America. 2006;103(8):2869 LP – 2873.

Bañuls AL, Sanou A, Van Anh NT, Godreuil S. Mycobacterium tuberculosis: Ecology and evolution of a human bacterium. Journal of Medical Microbiology. 2015;64(11):1261–9.

Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global?dissemination. proceeding of the national academy of sciences of the united states of America. 1997;94(18):9869 LP – 9874.

Lu B, Dong Hy, Zhao Xq, Liu Zg, Liu Hc, Zhang Yy, et al. A new multilocus sequence analysis scheme for Mycobacterium tuberculosis. Biomedical and Environmental Sciences. 2012;25(6):620–9.

Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLOS Biology. 2008;6(12):e311.

Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, et al. Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. Journal of Clinical Microbiology. 2007;45(1):39–46.

Gutacker MM, Mathema B, Soini H, Shashkina E, Kreiswirth BN, Graviss EA, et al. Single-nucleotide polymorphism–based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. Journal of the Infectious Diseases. 2006;193(1):121–8.

Keats BJB, Sherman SL. Chapter 13 - Population genetics. In: Rimoin D, Pyeritz R, Korf BBT-E and RP and P of MG, editors. Oxford: Academic Press; 2013. p. 1–12. www.sciencedirect.com/science/article/pii/B978012383834600015X

Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, et al. Out-of-Africa migration and neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics 2013;45(10):1176–82.

Reiling N, Homolka S, Walter K, Brandenburg J, Niwinski L, Ernst M, et al. Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice. MBio. 2013;4(4):e00250-13.

Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, et al. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. Journal of Clinical Microbiology. 2003;41(5):1963–70.

Bhargavi M. Multidrug Resistance in Tuberculosis: An overview. International Journal of Pharmaceutical. 2014;4(3):157–63.

Regmi SM, Coker OO, Kulawonganunchai S, Tongsima S, Prammananan T, Viratyosin W, et al. Polymorphisms in drug-resistant-related genes shared among drug-resistant and pan-susceptible strains of sequence type 10, Beijing family of Mycobacterium tuberculosis. International Journal of Mycobacteriology. 2015;4(1):67–72.

Brown T, Nikolayevskyy V, Velji P, Drobniewski F. Associations between Mycobacterium tuberculosis strains and phenotypes. Emerging Infectious Diseases. 2010;16(2):272–80.

Phylogeny magnitude of Mycobacterium tuberculosis based on genomic analysis

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Budi Yanti, Department of Pulmonology and Respiratory Medicine, School of Medicine, Universitas Syiah Kuala, Banda Aceh

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